uk.ac.sanger.psu.gfmerge.datacomp
Class GFMergeFeature

java.lang.Object
  extended by uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
All Implemented Interfaces:
GFMergeFeatureAble, LocateAble
Direct Known Subclasses:
GeneModel, SimFeature

public abstract class GFMergeFeature
extends java.lang.Object
implements GFMergeFeatureAble

abstract class which contains basic implementation of genemodels, blast and cDNA features.

Version:
1.0
See Also:
GeneModel, SimFeature

Field Summary
private  java.util.ArrayList exons
          ArrayList of exon within a genemodel
private  org.biojava.bio.seq.StrandedFeature feature
          BioJava feature object
private  java.util.ArrayList introns
          ArrayList of introns within a genemodel
 
Constructor Summary
GFMergeFeature(org.biojava.bio.seq.StrandedFeature feature)
          constructor which contains basic implementation for GeneModel and SimFeature objects
 
Method Summary
 java.util.ArrayList getExons()
          accessor method which returns ArrayList of exons
 org.biojava.bio.seq.StrandedFeature getFeature()
          accessor method which returns the appertaining StrandedFeature retrieved from file
 java.util.ArrayList getIntrons()
          accessor method which returns ArrayList of introns
 long getLength()
          accessor method which returns the length of the feature
 org.biojava.bio.symbol.Location getLocation()
          accessor method which returns Location of the BioJava feature
 org.biojava.bio.seq.StrandedFeature.Strand getStrand()
          accessor method which returns Strand of the BioJava feature
 long getTotalExonLength()
          accessor method which returns total exon length of the feature
private  void setExons(org.biojava.bio.seq.Feature _feature)
          accessor method which calculates exons of feature.
private  void setFeature(org.biojava.bio.seq.StrandedFeature _feature)
          accessor method which sets BioJava feature
private  void setIntrons(org.biojava.bio.seq.Feature _feature)
          accessor method which calculates introns of feature.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

feature

private org.biojava.bio.seq.StrandedFeature feature
BioJava feature object


exons

private java.util.ArrayList exons
ArrayList of exon within a genemodel


introns

private java.util.ArrayList introns
ArrayList of introns within a genemodel

Constructor Detail

GFMergeFeature

public GFMergeFeature(org.biojava.bio.seq.StrandedFeature feature)
constructor which contains basic implementation for GeneModel and SimFeature objects

Parameters:
feature - BioJava feature
Method Detail

getFeature

public org.biojava.bio.seq.StrandedFeature getFeature()
accessor method which returns the appertaining StrandedFeature retrieved from file

Specified by:
getFeature in interface GFMergeFeatureAble
Returns:
BioJava StrandedFeature

getExons

public java.util.ArrayList getExons()
accessor method which returns ArrayList of exons

Specified by:
getExons in interface GFMergeFeatureAble
Returns:
ArrayList of exons

getIntrons

public java.util.ArrayList getIntrons()
accessor method which returns ArrayList of introns

Specified by:
getIntrons in interface GFMergeFeatureAble
Returns:
ArrayList of introns

getLocation

public org.biojava.bio.symbol.Location getLocation()
accessor method which returns Location of the BioJava feature

Specified by:
getLocation in interface LocateAble
Returns:
Location of the BioJava feature

getStrand

public org.biojava.bio.seq.StrandedFeature.Strand getStrand()
accessor method which returns Strand of the BioJava feature

Returns:
Strand of the BioJava feature

getLength

public long getLength()
accessor method which returns the length of the feature

Specified by:
getLength in interface GFMergeFeatureAble
Returns:
length of the feature

getTotalExonLength

public long getTotalExonLength()
accessor method which returns total exon length of the feature

Specified by:
getTotalExonLength in interface GFMergeFeatureAble
Returns:
total exon length of the feature
See Also:
TotalExonLengthAnalysis

setFeature

private void setFeature(org.biojava.bio.seq.StrandedFeature _feature)
accessor method which sets BioJava feature

Parameters:
_feature - BioJava feature

setExons

private void setExons(org.biojava.bio.seq.Feature _feature)
accessor method which calculates exons of feature. Exon means sub Locations of BioJava feature.

Parameters:
_feature - BioJava feature

setIntrons

private void setIntrons(org.biojava.bio.seq.Feature _feature)
accessor method which calculates introns of feature. Intron means gaps inbetween sub Locations of BioJava feature.

Parameters:
_feature - BioJava feature